To put it simply, Kitty's stated reason for leaving Xavier's school in Ultimate Spider-Man doesn't jive with the events as we saw them in Ultimate X-Men. In USM, Kitty says the school was getting crowded, and Xavier was displeased with her for demanding he wipe Aunt May's mind of "Peter is Spider-Man" knowledge, so she transferred. In UXM, we've seen that Kitty's been thinking about leaving for at least a couple of issues (spanning a few days), and that Xavier's death has made her realize that being in life-or-death struggles for mutants isn't really what she wants. She came to Xavier's to learn control of her powers, she can control them, so she's leaving.
Sadly, my first feeling on reading Kitty's explanation in USM was disappointment. I thought, 'Darn it Bendis, Kitty just explained her reasons in Ultimate X-Men last month! Pay attention!' I know most of the books in the Ultimate Universe just do as they please, which is probably a good thing, since I wouldn't want other writers to have to pay attention to Ultimates. But I kind of liked that USM and UXM seemed to at least keep in touch. So, a seeming continuity gaffe was disheartening.
Then I thought about it a little more. Does Peter know Xavier is dead? He wasn't at the funeral, and given the hectic pace of his life, it's possible he's missed the news broadcasts about it. So, perhaps Kitty's not being totally straightforward with Peter. It could be payback for Peter going back to MJ, but that doesn't really seem to fit. So why?
In USM, the last time we see Kitty and Xavier interact, Kitty's telling Xavier she hates him because he won't go to bat for her, because taking people's memories is wrong (though I could swear Xavier has done that kind of stuff to people before. They were evil people I suppose, so that makes it okay, maybe?). So I figure that it was shortly after that disagreement when Xavier bites the dust (pending current events in Ultimate X-Men). So Kitty feels guilty. Things between the two of them didn't end on a positive note, and now she's feeling remorse over that. So she changes the story to where she left, but Xavier is still alive, which means they could patch things up again someday down the line.
Personally, I'd much rather go with that line of thinking, rather than "once again Marvel books can't keep their stories straight", so I will. Good for me.